I quit a PhD program in systems biology a few years back to become a programmer and now I contribute to an open source science project in systems biology in my free time. I feel like I am contributing far more to science now than I ever did as a grad student. After spending a couple of years in industry, I (undeservedly) feel like an engineering god working on this project. It's not that scientists aren't smart, it's that they haven't worked in a place where good engineering practices are vital, rather they have worked in the academic world where you typically hack together a bunch code that barely works, write a paper, and call it a day. Today science is at a point where many, if not most questions are answered with computers, and IMO there is a huge need for quality engineers to produce that software.

The challenge is finding a fair way to compensate talented engineers. Many might do it for free under a "code for science" campaign. But that would require a lot of scientist to realize and then admit how deeply incompetent they are at programing.

I know very few scientists who are terribly pleased with their coding skills, and many who actively admit they're not great coders.

The problem is you can't rely on a "code for science" campaign. A research study isn't something done in a weekend Hackathon, though they are occasionally helpful. What happens if, 2 years into your 5 year study, your helpful volunteers, leaving you with an incomplete code base beyond your skills to maintain or extend?

I know of two ways currently being tried to address this.

The first is to have scientists break their problems down into chunks that can be performed by volunteers but which aren't completely beyond the ability of the scientist to manage the resultant code. This is doable for much of physics and computational biology, less so where a scientist isn't a programmer themselves. We're taking this approach with http://solvers.io.

The second is to have the scientists mentored by programmers to help them become better at it. This is the approach being taken by http://interdisciplinaryprogramming.com.

In both cases, any particular volunteer dropping out is probably not a massive blow. If a project is going to rely on a particular programmer long-term, they probably need to find the funding to pay them.

I would love to see smaller, more puzzle like challenges on solvers.io .. I love the idea but a lot of the projects are kind of big!

I'm really interested in solvers.io, and I've been trying to come up with things like that. Small, bite-sized chunks that take just a bit of time, and then everyone can go their separate way.

Thanks! This is our number one priority at the moment. We'll have a new small-task focused design up in a few weeks and are working with project owners to break things down.

There are a reasonable number of people in my area (mostly, game AI and AI-for-game-design) who either left academia, or never were in it, but still attend conferences and publish papers. Those outside academia typically publish a bit less, mostly due to either having day jobs or pretty booked consulting careers (and in a few cases, due to secretive employers restricting what they can publish). But many are still actively involved in conferences like http://www.aiide.org.

It doesn't seem mostly billed as "escaping" or "rebelling", though. Just, some people find different careers more attractive. Some people would hate some of the bullshit involved in academia but find consulting attractive; other people would hate some of the bullshit involved in consulting but find an academic job attractive; and other people do something else entirely, like working at Electronic Arts. People end choosing a pretty wide range of different careers, all with tradeoffs. Some people choose more than one! If anything, kind of amusingly, the narrative is a bit more frequent in the other direction: people who had a senior job at a big game company and "rebelled" or "escaped" by quitting the six-figure job and going back to school for a PhD. For example, the AI lead on No One Lives Forever 2 and F.E.A.R. left the AAA game industry to get a PhD... and now is leaving academia again to go back into the game industry, but as an indie (http://web.media.mit.edu/~jorkin/).

I get the impression a lot of applied CS has those kinds of dynamics. If you go to a systems, graphics, data-mining, etc. conference, there's a good mix of big-company, freelance, and academic people, and a number of people who've worn more than one of those hats.

I have only a Bachelors (math) and work at a non profit research institute as a software engineer. I've contributed to a number of publications and first authored one, and had my name on some grant applications so I guess I count as an academic.

I think the bio field is desperate for people with software skills and it is actually pretty easy to get into if your willing to take a pay cut vs industry software rates.

On the other hand, I was getting recruited by a machine learning company based on my open source contributions etc but interest dropped off when they found out I didn't have a PHD (and wouldn't move to the bay area).

I think the reality of bio research is that it does involve a ton of mundane work and that even when working on a novel project we spend a lot of time doing server admin, cleaning, processing, reformatting data, building databases and data portals etc. Every time the scale of a study increases one of our tools breaks and getting things to scale often involves more hacking then pure research.

Occasionally one of us engineers come up with a novel approach worth publishing and more often we make a contribution to a larger study that is novel biology even if it isn't novel analytically.

I would contrast this with, say, machine learning researchers chasing percentage points on well established data sets like MINST or even doing kaggle competitions. Our data tends to be less settled more noisy, heterogenous, missing etc and have questions that are less well posed (eg often one disease is actually many with similar symptoms) so there is a lot more mundane wading through things.

I'm not sure what my prospects are if/when I decide to change jobs but I'm hoping that my open source contributions and papers would convince an employer that I know what I'm doing enough to continue working on novel problems.

1. The field can be desperate for software engineers. OR 2. You need to take a pay cut if you want to join this field.

If it's both, someone at the top is very out of touch.

You have to realize that most post-doc's, so people who are in their 30's-40's and have the years of tenure and education as a doctor with residency make like $45-50K; that is, if they're lucky to get it.

So for a code monkey to come in and tap away on his stupid keyboard to make like $75K is a travesty as far as the research academia is concerned.

But in research, you're better than the sell-out's trying to make people click on ads and shit though. So part of your paycheck every week is padded with tokens of self-righteousness and moral superiority that you can redeem in times of needed philosophical consolations.

Post docs in UC schools are unionized (as well as elsewhere).

It is both. And the people at the top are various grant funding agencies that often move at the pace of government and are used to the post doc pay scale. Things are changing but the salaries places like google and amazon pay are just hard to match on a government grant.

Academia, because it is fueled by grants, cannot necessarily adjust pay to compete with the demand from other sectors, no matter how much they might like to.

Beyond that, good programmers are stupidly helpful, but not mission-critical.

I would work on research projects for free, if the projects were interesting and/or I got some reputation out of it.

If you're interested in doing research without an affiliation, I'm building up a network of collaborators for open research. Have a ton of interesting problems around bioinformatics and computational biology. I've put a couple on http://solvers.io, but if you just want to chat drop me an email.

Does no affiliation generally translate to no funding? In my experience in physics, the lack of affiliation per se isn't a terrible barrier. All papers since 1992 are available for free on the arXiv, and journal editors actually make a pretty honest effort to evaluate unaffiliated authors based on the merits of the manuscript. (Of course, most unaffiliated submissions are of low quality, so it's hard to avoid a bit of prior probability slanted against them.)

Funding seems pretty impossible if you're unaffiliated, though.

> Funding seems pretty impossible if you're unaffiliated, though.

In CS (I am unfamiliar with other areas), I'll agree that the really big grants usually go to academic institutions, big defense contractors, or consortia of the two. But there are pretty decent funds set aside specifically for small businesses, using funds that Congress has earmarked to the National Science Foundation exclusively for such a purpose. Last I saw, the success rate for applying for such funds (in terms of % of applications successfully funded) was actually higher than for academic applicants, though the total awards are smaller.

You do have to convince a funder that your independent research organization is serious and capable of delivering research. But if you can do so, in the U.S. there are two NSF programs specifically targeting research money towards small businesses. The first is the Small Business Technology Transfer Program (STTP). This requires two organizations, with a small business and an academic institution submitting a joint proposal. They propose a plan for taking current academic results and turning them into viable products that will support a small business. The idea is to give money that will enable the academia-industry barrier to be crossed, with one partner on each side who explains why they are a good team for making the crossing happen. The second is the Small Business Innovation Research (SBIR) program, which small business can apply solo to. This funds activities that take place wholly in the private sector, but present a credible research plan that the evaluators consider to have a high likelihood of producing scientifically interesting results.

Funding is harder if you're unaffiliated - unless you collaborate with people in academia. There are more ways to do this opening up though, crowd funding (http://experiment.com) for example.

How common is it for experiment.com funding to include labor? Most of the projects I checked look like they're just covering equipment and travel, and that's not going to be enough to work on the project full time.

I'm trying to escape academic neuroEconomcs right now. I was shocked by how much nepotism and how little merit there is in academic science. I'm pursuing a research agenda about 'learning' on my own. I built an free API that uses neuroscientific learning models to help developers make apps sticky. I expect that the optimization algorithms I'm using will lead to new findings in how brains learn.

Interesting, could you point out the open lab notebook wiki's? I'm looking to do that with IPython notebooks.

In Boston, we're looking to revitalize DIY bio at BOSSlab http://bosslab.org/

I remember that a significant part — up to a fifth, I would say — of the researchers and lecturers whose seminars I followed in the late 80s in France, either did not hold a doctorate or used to publish a big thing only once in a while but were nonetheless respected by their peers for their knowledge and commitment to science, and enjoyed secure academic positions. Nowadays, surviving in the academy without a PhD (or even, in countries like Germany, without the higher "habilitation") and without abiding to the "publish or perish" rule has become increasingly unrealistic.

But it still happens, albeit at the margins. I have been working myself as a scientist in the academy for the last twenty years and even held assistant professorship positions in prestigious universities in Germany for almost ten years without a PhD and without much publications. In my case, that was most of the time due to a combination of factors: 1) the need for an outsider in the lab (particularly to avoid conflicts over scarce tenured professorship positions) 2) being able to teach and research topics for which more than one person would have been needed otherwise 3) being (a little) known in the field, and known as eccentric but proficient at the job.

Funding is certainly an issue. You do need an academic affiliation (at least a formal one) to apply for grants. But I do not feel I have been less successful in securing funding from European and German research funds than colleagues with PhDs and habilitations and lots of publications. As soon as past projects were successfully completed, it has never been a big issue. The real problem is that in my field only fashionable and pointless projects are being funded lately.

As a consequence, I have come to carry my research almost completely independently. Coding and data analysis for private corporations and casual teaching at the university pay the bills. From time to time, I still rely on academic grants to fund field research. My wife and I work together and we have a very spartan way of life, dedicated to science and study.

Doing science at the margins of the academy implies its share of abnegation, is certainly viewed as bizarre by many but it happens. Although I do not complain, I won't recommend it either.

Hey, I'm extremely interested in open source computational biology/biochemistry and find this very interesting. What do you do to make money whilst exploring and contributing to these areas?

I've had somewhat the opposite experience - I left academia (math) and am very happy to do programming for a living on so-called mundane CRUD apps.

Academia suffocates you with its processes, and the tendency of it to zombify young academics to thinking that high abstraction is the only way to go in life is in itself horrible.

In the end, I'm happy doing what I do. Mathematics was a fun challenge, but I never viewed myself as just a mathematician - I have a deep thinking highly adaptable mind that is geared to solve problems, not just be a specialist.

I decided not to pursue and English degree because yeah right I'm not paying tuition for that, not after all the debt I accumulated from my CS undergrad.

It basically means that continental philosophy is my hobby. I try to keep up with 'real' academia through following certain people on Twitter, and submitting papers to conferences, reading things...

Your PLOS stuff sounds really interesting! Could you point me to some of that please?

Whilst plugging away at my thesis I have gotten interested in data analysis, data mining, etc. and my default data set consists of PLOS articles. I blog about stuff I do here: http://georg.io

There is a fair bit of space in between PhD research and CRUD work.

Industrial Research can be on stuff that will lead to products in the near future. I think you can get a lot of the same feel of academic research by working on things like international standards. I have been able to do this without even a bachelors degree.